Understanding and rewiring cellular behavior with synthetic biology approaches

项目摘要 人体生理学依赖于细胞对环境信号的精确反应。响应的特异性 环境信号是通过特定的蛋白质组学，转录组学，表观基因组学和非遗传学来实现的。 细胞状态。在生理状态下，健康细胞与周围组织协调运作， 响应环境刺激的特定功能。在疾病中，细胞状态的失调可以防止 细胞产生必要的反应，并导致独立于生理环境的增殖。 了解细胞状态如何驱动细胞功能对于了解健康组织功能至关重要， 疾病，并需要工程细胞疗法能够编码的特定行为，其目标 环境.尽管对单细胞生物学进行了数十年的研究，但我们仍然不了解 将细胞状态与细胞对环境的特异性反应联系起来的原理 在我提议的研究中，我将使用合成生物学工具来定量探测 细胞状态和信号特异性之间的联系我提出的工作将提供深入了解细胞如何 不同类型的人对他们的环境有独特的反应，并将产生计算模型， 可以用来设计细胞行为。为了研究不同类型的细胞如何独特地响应 同样的信号，我将使用光遗传学来干扰早期候选细胞类型中的模型信号cAMP。 小鼠胚胎和发育中的斑马鱼的无偏筛选。我对小鼠胚胎干细胞的研究 将作为通过细胞内信号传导控制细胞类型和重新连接细胞的原理的证明。 基因表达程序的反应。我对斑马鱼的研究将产生一个预测模型， 用于仅使用来自该细胞的转录数据来推断给定细胞对刺激的独特反应。 在整个工作中，我将专注于生成可解释的计算模型， 来设计细胞行为。 我将通过综合我以前在神经科学，细胞信号传导， 并应用合成生物学，建议在发育生物学，基因组学，定量 细胞过程建模和细胞工程。我也会补充我以前的训练， 在教学和辅导方面的经验，以及在宣传方面的新培训，使我能够最好地指导我的 未来的学员和进一步的正义，多样性，公平，并在整个科学事业的包容性。通过 我的研究和培训，我将很好地过渡到一个独立的位置，我 可以实现我的科学和宣传目标。

PROJECT SUMMARY Human physiology depends on precise cellular responses to environmental signals. Specificity in responding to environmental signals is achieved through specific proteomic, transcriptomic, epigenomic, and non-genetic cell states. In physiological states, healthy cells function in harmony with their surrounding tissues, performing specific functions in response to environmental stimuli. In disease, dysregulation of cell state can prevent cells from producing necessary responses and lead to proliferation independent of physiological context. Understanding how cell state drives cell function is essential for understanding tissue function in health and disease, and is required for engineering cell therapies capable of specific behaviors encoded by their target environments. Despite decades of research into single cell biology, we still don't understand the fundamental principles that connect cell state with specificity in cellular responses to their environment In my proposed research, I will use synthetic biology tools to quantitatively probe the connection between cell state and signaling specificity. My proposed work will provide insight into how cells of different types achieve unique responses to their environments and will generate computational models that can be used to engineer cellular behavior. To investigate how cells of different types uniquely respond to the same signal, I will use optogenetics to perturb the model signal cAMP in candidate cell types of the early mouse embryo and in an unbiased screen in developing zebrafish. My studies in mouse embryonic stem cells will serve as a proof of principle for controlling cell type through intracellular signaling and for rewiring cellular responses with genetic expression programs. My work in zebrafish will result in a predictive model that can be used to infer a given cell's unique response to a stimulus using only transcriptional data from that cell. Throughout this work, I will focus on generating interpretable computational models that can be used in the future to engineer cellular behavior. I will achieve the above work through synthesizing my previous training in neuroscience, cell signaling, and applied synthetic biology with proposed training in developmental biology, genomics, quantitative modeling of cellular processes, and cellular engineering. I will also supplement my previous training and experience in teaching and mentorship with new training in advocacy to best position myself to mentor my future trainees and further justice, diversity, equity, and inclusion throughout the scientific enterprise. Through my proposed research and training, I will be well positioned to transition to an independent position where I can achieve my scientific and advocacy goals.